The mother, who had business opportunities and family support in the Gold Coast, was devastated that the father - who she says pays just $8 a week towards their upbringing - could force them to stay.
But the Family Court, which decides 400 such cases a year, is unrepentant, saying parents who want to move away must be committed to maintaining the children's relationship with the other parent.
The controversial decision shows that even when a relationship is destructive and abusive, women have to stay in New Zealand because of the children's attachment to their father.
Judge Robert Murfitt said he understood why the woman wanted to get away from the father whom he described as "feckless and faithless" but he said the children, aged eight and six, loved their dad and would lose contact with him if they moved.
Acting principal Family Court judge Paul von Dadelszen said judges found relocation cases "extremely difficult to decide" but had to put the children's interest first.
The Sunday Star-Times cannot name the parents, the children or the North Island city in which they live.
Murfitt said there were faults with both parents and he told them to stop fighting because they were damaging their children.
The children's love of their mum and dad surprised the judge given the verbal abuse and physical violence they had seen in their parents' "torrid" relationship.
He criticised the father for making his children keep secrets when they visited his girlfriend.
The mother described her ex-partner as a "loser", whom she couldn't trust to protect the children because he allowed his drunk uncle to sleep in the same bed as his young daughter.
The judge ordered the father to do a parenting course, saying his relationship with the children could otherwise become so non-existent it would not stop the family court allowing a move overseas in the future.
In another recent relocation decision, the Court of Appeal ordered a New Zealand mother to return to Australia despite her and her children having a protection order against their father.